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Sholl Analysis arbor value differences

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Sholl Analysis arbor value differences

jstanko
6 posts
I need help clarifying the differences in Advanced Sholl Analysis output depending on which arbor value I use.  

I'm using a binarized (background=0) skeleton image and when I place the starting point on the path (as described on http://fiji.sc/wiki/index.php/Simple_Neurite_Tracer:_Sholl_analysis) I get the following output:
java.lang.ArrayIndexOutOfBoundsException: 255
        at Advanced_Sholl_Analysis.run(Advanced_Sholl_Analysis.java:162)
        at ij.IJ.runUserPlugIn(IJ.java:184)
        at ij.IJ.runPlugIn(IJ.java:151)
        at ij.Executer.runCommand(Executer.java:127)
        at ij.Executer.run(Executer.java:64)
        at java.lang.Thread.run(Thread.java:619)

If I place the starting point off the path, I have the option of selecting the arbor value (0, 255), but I get two different outputs depending on which value I choose.  The arbor value of the image on the left is 0 and the value of the image on the right is 255.  

1.  Am I correct in assuming that the difference is where the center of the rings is generated (the closest point with the same/different value as the defined arbor value)?

2.  Why are the Intersections Masks different?

3.  Does it matter which value I use and why?

Thanks in advance for your help!

arbor values